If you take "atemi" to mean nage is striking uke with a hand of foot or what have you. Then either: O-sensei was bad with percentages, or none of us are doing Aikido, or we have misunderstood his meaning. Western boxing is barely 90% atemi, there are lots of strikes, but there are also a lot of footwork drills, covering technique. Most styles of Karate are probably not "90%" atemi, there are a few throws, and blocks etc. If your direct meaning is 90% of the Aikido syllabus is made up of atemi, then something is wrong, because it's not. If you mean to say that Aikido forms use atemi 90% of the time, (meaning you will see an atemi happen in 90% of the techniques) , and you take 90% to mean only a lot, and not litteraly 90%, this could be correct, because a lot of them do, still not 90%, but quite a few do.

What separates Aikido from other martial arts? Is it simply the technical syllabus? I believe O-sensei's idea of what Aikido went far beyond it's shihonage's, kotegaishi's, and other simply technical aspects. I believe that he was truly interested in studying "Aiki". I think you could have giving O-sensei any technical syllabus, and he still would have formed "Aikido". Weather he had been purely a Karate man, or a kendoka, or what ever, he would have still invented "Aikido". True Aikido is not attached to the 7 throws, and 6 controls, it is only attached to the idea of "Aiki". Find what Aiki is and I'm sure you'll find the answer to "Aikido is 90% atemi".